1
|
Pham M, Lu X, Rana A, Osher S, Miao J. Real space iterative reconstruction for vector tomography (RESIRE-V). Sci Rep 2024; 14:9541. [PMID: 38664487 PMCID: PMC11045750 DOI: 10.1038/s41598-024-59140-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Tomography has had an important impact on the physical, biological, and medical sciences. To date, most tomographic applications have been focused on 3D scalar reconstructions. However, in some crucial applications, vector tomography is required to reconstruct 3D vector fields such as the electric and magnetic fields. Over the years, several vector tomography methods have been developed. Here, we present the mathematical foundation and algorithmic implementation of REal Space Iterative REconstruction for Vector tomography, termed RESIRE-V. RESIRE-V uses multiple tilt series of projections and iterates between the projections and a 3D reconstruction. Each iteration consists of a forward step using the Radon transform and a backward step using its transpose, then updates the object via gradient descent. Incorporating with a 3D support constraint, the algorithm iteratively minimizes an error metric, defined as the difference between the measured and calculated projections. The algorithm can also be used to refine the tilt angles and further improve the 3D reconstruction. To validate RESIRE-V, we first apply it to a simulated data set of the 3D magnetization vector field, consisting of two orthogonal tilt series, each with a missing wedge. Our quantitative analysis shows that the three components of the reconstructed magnetization vector field agree well with the ground-truth counterparts. We then use RESIRE-V to reconstruct the 3D magnetization vector field of a ferromagnetic meta-lattice consisting of three tilt series. Our 3D vector reconstruction reveals the existence of topological magnetic defects with positive and negative charges. We expect that RESIRE-V can be incorporated into different imaging modalities as a general vector tomography method. To make the algorithm accessible to a broad user community, we have made our RESIRE-V MATLAB source codes and the data freely available at https://github.com/minhpham0309/RESIRE-V .
Collapse
Affiliation(s)
- Minh Pham
- Department of Physics and Astronomy and California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA.
- Department of Mathematics, University of California, Los Angeles, CA, 90095, USA.
- Institute of Pure and Applied Mathematics, University of California, Los Angeles, CA, 90095, USA.
| | - Xingyuan Lu
- Department of Physics and Astronomy and California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
- School of Physical Science and Technology, Soochow University, Suzhou, 215006, China
| | - Arjun Rana
- Department of Physics and Astronomy and California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Stanley Osher
- Department of Mathematics, University of California, Los Angeles, CA, 90095, USA
- Institute of Pure and Applied Mathematics, University of California, Los Angeles, CA, 90095, USA
| | - Jianwei Miao
- Department of Physics and Astronomy and California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA.
| |
Collapse
|
2
|
Xu S, Dunlop DJ, Newell AJ. Micromagnetic modeling of two-dimensional domain structures in magnetite. ACTA ACUST UNITED AC 2012. [DOI: 10.1029/94jb00137] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
3
|
|
6
|
Fukuma K, Dunlop DJ. Three-dimensional micromagnetic modeling of randomly oriented magnetite grains (0.03-0.3μm). ACTA ACUST UNITED AC 2006. [DOI: 10.1029/2006jb004562] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Koji Fukuma
- Department of Environmental System Science; Doshisha University; Kyotanabe Japan
| | - David J. Dunlop
- Geophysics, Physics Department; University of Toronto; Toronto, Ontario Canada
| |
Collapse
|
7
|
Schepper W, Schotter J, Brückl H, Reiss G. Analysing a magnetic molecule detection system--computer simulation. J Biotechnol 2005; 112:35-46. [PMID: 15288939 DOI: 10.1016/j.jbiotec.2004.04.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Revised: 04/19/2004] [Accepted: 04/19/2004] [Indexed: 10/26/2022]
Abstract
The detection of single molecules, e.g. in biology is possible by marking the interesting molecules with magnetic beads and detect the influence of the beads on giant magnetoresistance (GMR)/tunnel magnetoresistance (TMR)/spin valve (SV) sensors. The development of suitable multilayers has been studied experimentally as well as theoretically in order to optimize the sensor parameters. A finite difference (FD) method including the usually used contributions to the total energy [exchange, antiferromagnetically (af) coupling, anisotropy and magnetostatic] is used for the simulation with additional contributions to the local field according to the stray fields of the beads. In this work, we will show the results of micromagnetic calculations of the magnetization behavior of GMR/TMR sensors considering also the interaction between the domains in the magnetic layers of the sensor and the bead area. We can present first calculations where the bead particles (signal source) and the magnetic layers (sensor device) are considered as a whole magnetic ensemble.
Collapse
Affiliation(s)
- W Schepper
- Department of Physics, University of Bielefeld, Universitätsstrasse 25, 33501 Bielefeld, Germany.
| | | | | | | |
Collapse
|
9
|
Newell AJ, Merrill RT. Size dependence of hysteresis properties of small pseudo-single-domain grains. ACTA ACUST UNITED AC 2000. [DOI: 10.1029/2000jb900122] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
10
|
Newell AJ, Merrill RT. Single-domain critical sizes for coercivity and remanence. ACTA ACUST UNITED AC 1999. [DOI: 10.1029/1998jb900039] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
12
|
Foss S, Moskowitz BM, Proksch R, Dahlberg ED. Domain wall structures in single-crystal magnetite investigated by magnetic force microscopy. ACTA ACUST UNITED AC 1998. [DOI: 10.1029/98jb00152] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
14
|
Pokhil TG, Moskowitz BM. Magnetic domains and domain walls in pseudo-single-domain magnetite studied with magnetic force microscopy. ACTA ACUST UNITED AC 1997. [DOI: 10.1029/97jb01856] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
15
|
Özdemir Ö, Dunlop DJ. Effect of crystal defects and internal stress on the domain structure and magnetic properties of magnetite. ACTA ACUST UNITED AC 1997. [DOI: 10.1029/97jb01779] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
16
|
Dunlop DJ, Argyle KS. Thermoremanence, anhysteretic remanence and susceptibility of submicron magnetites: Nonlinear field dependence and variation with grain size. ACTA ACUST UNITED AC 1997. [DOI: 10.1029/97jb00957] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
17
|
Fukuma K, Dunlop DJ. Monte Carlo simulation of two-dimensional domain structures in magnetite. ACTA ACUST UNITED AC 1997. [DOI: 10.1029/96jb03663] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
18
|
Newell AJ, Williams W, Dunlop DJ. A generalization of the demagnetizing tensor for nonuniform magnetization. ACTA ACUST UNITED AC 1993. [DOI: 10.1029/93jb00694] [Citation(s) in RCA: 178] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|